I feel like I have a decent handle on the ending now that I've thought about it for awhile. I'm like 70-80% of the way there. Here's my interpretation as of now:
Cooper asks Jefferies to send him back in time to the night Laura dies as that was the night that started all of this. He is successful (we see her body disappear) but then Judy angrily intervenes, through Sarah Palmer.
I 100% subscribe to the theory that Sarah is host to Judy through the frogmoth. Visually the scene where she opens her face both looks similar to the moth creature and the creature in the box (who I also believe is Judy). Also I rewatched a clip of episode 8 and noticed something I completely forgot about. After the frogmoth goes in the girl's mouth, the woodsman stops his broadcast and walks outside and disappears into the darkness. As he does that there is a faint sound effect of a horse neighing. The white horse is seen twice in the history of the show, both times by Sarah Palmer. The exact meaning of the horse I'm not completely decided on, but no doubt about it that it's linked heavily to Sarah. The other big clue to this is in the final episode after Bad Coop goes through the portal and gets caught in that cage in the White Lodge/Movie Theater/Whatever the Giant changes the destination from the Palmer house to the Sheriff's station. Bad Coop was looking for the Palmer house. In episode 1, Bad Coop shows the image of the black circle with antenna looking things (which we also see on Hawk's map) and says that is what he is looking for. As many people pointed out, the figure that vomits up BOB and the eggs has similar antenna to that image. All of these things are Judy. Bad Coop was looking for Judy at Sarah Palmer's house. Not totally sure on why, maybe to destroy her and take her place? Or just never have to go back to the Lodge? Not clear.
Anyway, we see Cooper leading Laura away from her murder and the events starting to undo themselves, when suddenly she screams and disappears. We then cut to the scene of Sarah smashing the picture frame of Laura. Judy is seeing what Cooper is doing and sending her away to another world where she becomes Carrie Page. The Fireman gives Cooper the information to go find her (first scene of episode 1) and him and Diane drive the 430 miles and enter the other world. The other world is under Judy's control. We see the diner named Judy's. The people in it are horrible and evil (truckers harassing the waitress, Carrie Page's horrible life complete with a dead body in her living room). And the existence of the Chalfonts/Tremonds suggest this is part of or related to the lodge. I think it's some sort of hell or prison maybe?
The biggest thing I am unclear on, is Diane's role in all of this, and specifically the sex scene. It's purpose and meaning eludes me completely. Most of the theory from waggish.org I don't buy much at all, but the idea of the sex scene being a way to summon Judy ala the black box sex scene is the closest thing to a plausible theory I've heard but I'm not totally sold on it.
Some other assorted thoughts: Audrey "waking up" in the Roadhouse, is that white room the same world Carrie, Richard, and Linda are in? We live inside a dream. Audrey woke up from the dream. Also, Jefferies saying "Say hi to Gordon for me, he will remember the unofficial version". This reads to me as seeding for a possible season 4 or movie. Cooper needs to find Gordon in the alt-world. He will remember Twin Peaks. If they were to continue the show, would the show be about Cooper, Laura, and Cole all trying to get back home? Maybe we would see alternate versions of all the Twin Peaks cast playing different characters? Although these might go against the alt-world being part of the lodge or created by Judy.
Feel free to poke any holes in this if you see any. Seems pretty solid to me. I think I'll have an even better handle once I rewatch the whole show from front to back.